Influence of Mn²⁺ ion coordination on tRNAVal₁ macrostructure and determination of some coordination sites of Mn²⁺ ions in tRNAVal₁

Electron paramagnetic resonance spectroscopy has been used to study the coupling of Mn 2+ ions with the tRNA Val 1 modified with a spin label at four pseudouridylic residues and with the valyl‐tRNA Val 1 modified with a spin label at the α‐amine group of the valyl residue. A sharp increase of spin‐label mobility has been found in these samples, due to the conformational transition induced by the first and second Mn 2+ ions. Analysis of dipole–dipole couplings of spin labels with the coordinated ions revealed a definite order in the occupation of ion coordination sites in the tRNA. For some valyl‐tRNA Val 1 molecules, the second Mn 2+ ions were shown to coordinate on the α‐amine group of the valyl residue at a distance of 15–25 Å from a spin label. As a result of the conformational transition, a coordination site appeared in the tRNA at one of the pseudouridylic residues, its distance from the spin label being less than 10 Å. It has been suggested that the conformational transition induced by ions excluded some bases from the system of hydrogen bonds at the level of the tRNA tertiary structure. As a result, these bases acquired sufficient sterical freedom to participate in the Mn 2+ ion coordination.